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21  structures 439  species 1  interaction 498  sequences 4  architectures

Family: SRP19 (PF01922)

Summary: SRP19 protein

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

SRP19 protein Provide feedback

The signal recognition particle (SRP) binds to the signal peptide of proteins as they are being translated. The binding of the SRP halts translation and the complex is then transported to the endoplasmic reticulum's cytoplasmic surface. The SRP then aids translocation of the protein through the ER membrane. The SRP is a ribonucleoprotein that is composed of a small RNA and several proteins. One of these proteins is the SRP19 protein [1] (Sec65 in yeast [2,3]).

Literature references

  1. Lingelbach K, Zwieb C, Webb JR, Marshallsay C, Hoben PJ, Walter P, Dobberstein B; , Nucleic Acids Res 1988;16:9431-9442.: Isolation and characterization of a cDNA clone encoding the 19 kDa protein of signal recognition particle (SRP): expression and binding to 7SL RNA. PUBMED:2460823 EPMC:2460823

  2. Hann BC, Stirling CJ, Walter P; , Nature 1992;356:532-533.: SEC65 gene product is a subunit of the yeast signal recognition particle required for its integrity. PUBMED:1313947 EPMC:1313947

  3. Stirling CJ, Hewitt EW; , Nature 1992;356:534-537.: The S. cerevisiae SEC65 gene encodes a component of yeast signal recognition particle with homology to human SRP19. PUBMED:1313948 EPMC:1313948


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002778

The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [PUBMED:17622352, PUBMED:16469117]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor [PUBMED:17507650]. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 [PUBMED:12364595].

This entry represents the SRP19 subunit. The SRP19 protein is unstructured but forms a compact core domain and two extended RNA-binding loops upon binding the signal recognition particle (SRP) RNA [PUBMED:17434535].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(77)
Full
(498)
Representative proteomes NCBI
(512)
Meta
(73)
RP15
(106)
RP35
(190)
RP55
(274)
RP75
(335)
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Format an alignment

  Seed
(77)
Full
(498)
Representative proteomes NCBI
(512)
Meta
(73)
RP15
(106)
RP35
(190)
RP55
(274)
RP75
(335)
Alignment:
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Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(77)
Full
(498)
Representative proteomes NCBI
(512)
Meta
(73)
RP15
(106)
RP35
(190)
RP55
(274)
RP75
(335)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Enright A
Previous IDs: none
Type: Family
Author: Enright A, Ouzounis C, Bateman A
Number in seed: 77
Number in full: 498
Average length of the domain: 93.80 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 54.93 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.7 21.7
Trusted cut-off 21.7 21.9
Noise cut-off 21.6 21.6
Model length: 95
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

SRP_SPB

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the SRP19 domain has been found. There are 21 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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